Behavioural neuroscience data wrangling and analysis tools
Execute the following from the project folder in a shell with conda on the path:
conda env create -f environment.yaml
conda activate behapy
pip install -e .To use behapy, the TDT proprietary formatted source data needs to first be converted BIDS-like raw data format. This assumes session_map.csv is in the sourcedata_root folder:
tdt2bids [session_fn] [experiment_fn] [bidsroot]
Alternatively, you can specify the source data directory with --sourcedata_root. (Note that this path is relative to session_fn and not the current directory.):
tdt2bids [--sourcedata_root sourcedata_root] [session_fn] [experiment_fn] [bidsroot]
This will output raw data files in
[bidsroot]/rawdata
Next open the preprocessing dashboard and identify regions of the recording for exclusion from analysis:
ppd [bidsroot]
The preprocessing dashboard will open in a browser window. Select a recording by index to pull up an interactive bokeh plot of raw fluorescence and normalised fluorescence. Then use the box-select tool to exclude time points from analysis.
Finally, write the preprocessed data to the [bidsroot]/derivatives/preprocess tree:
preprocess [bidsroot]
A sample annotated analysis pipeline is available in examples/analyse.ipynb
There is a MedPC event reading example in examples/showevents.ipynb
behapy is maintained by Chris Nolan.
This project would not exist without the energetic contributions from folks in the BrainHack community. Thanks in particular to: